Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008621.1 Hibiscus syriacus cultivar Beakdansim tig00111584_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1991651
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 11
Found at i:1733601 original size:23 final size:23
Alignment explanation
Indices: 1733548--1733602 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
1733538 TTTTTAAACC
* *
1733548 TTTATATAATTTTTTAATAATTA
1 TTTATTTAATCTTTTAATAATTA
*
1733571 TTTATTTAATCTTTTAATATTTA
1 TTTATTTAATCTTTTAATAATTA
*
1733594 TTTTTTTAA
1 TTTATTTAA
1733603 CCTTAATATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTATTTAATCTTTTAATAATTA
Found at i:1734054 original size:20 final size:20
Alignment explanation
Indices: 1734029--1734102 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
1734019 TTTTCCCAAT
*
1734029 TCACAATGCGAATAAGTAAA
1 TCACAACGCGAATAAGTAAA
** *
1734049 TCACAACGCGAATTGGGAAAA
1 TCACAACGCGAA-TAAGTAAA
** *
1734070 TTGCAATGCGAATAAGTAAA
1 TCACAACGCGAATAAGTAAA
*
1734090 TCGCAACGCGAAT
1 TCACAACGCGAAT
1734103 TGGGAAAATC
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 27 0.66
21 14 0.34
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (20 bp):
TCACAACGCGAATAAGTAAA
Found at i:1734077 original size:41 final size:41
Alignment explanation
Indices: 1734032--1734121 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
1734022 TCCCAATTCA
*
1734032 CAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAATTG
1 CAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAATCG
*
1734073 CAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAATCG
1 CAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAATCG
1734114 CAATGCGA
1 CAATGCGA
1734122 TACTGACTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (41 bp):
CAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAATCG
Found at i:1734080 original size:21 final size:21
Alignment explanation
Indices: 1734046--1734121 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
1734036 GCGAATAAGT
* *
1734046 AAATCACAACGCGAATTGGGA
1 AAATCGCAATGCGAATTGGGA
* ** *
1734067 AAATTGCAATGCGAA-TAAGT
1 AAATCGCAATGCGAATTGGGA
*
1734087 AAATCGCAACGCGAATTGGGA
1 AAATCGCAATGCGAATTGGGA
1734108 AAATCGCAATGCGA
1 AAATCGCAATGCGA
1734122 TACTGACTAT
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
AAATCGCAATGCGAATTGGGA
Found at i:1734134 original size:41 final size:41
Alignment explanation
Indices: 1734052--1734182 Score: 115
Period size: 41 Copynumber: 3.2 Consensus size: 41
1734042 AAGTAAATCA
* * *
1734052 CAACGCGAATTGGGAAAATTGCAATGCGAATA-AGTA-AATCG
1 CAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACTATCG
1734093 CAACGCGAATTGGGAAAATCGCAATGCGATACTGACTATCG
1 CAACGCGAATTGGGAAAATCGCAATGCGATACTGACTATCG
* * ** * * * *
1734134 CAATGCGATAAT-ACAAAATCGCAACGAGATACTTACTTTCG
1 CAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACTATCG
1734175 CAACGCGA
1 CAACGCGA
1734183 TACTGACTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
40 4 0.05
41 69 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
CAACGCGAATTGGGAAAATCGCAATGCGATACTGACTATCG
Found at i:1734135 original size:20 final size:20
Alignment explanation
Indices: 1734110--1734224 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
1734100 AATTGGGAAA
*
1734110 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1734130 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
1734151 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
1734171 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
1734191 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1734211 TTCGCAACGCGATA
1 ATCGCAACGCGATA
1734225 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1734183 original size:41 final size:41
Alignment explanation
Indices: 1734107--1734244 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
1734097 GCGAATTGGG
* * *
1734107 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
1734148 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
1734190 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
1734229 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
1734245 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.39
41 44 0.56
42 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:1734440 original size:22 final size:22
Alignment explanation
Indices: 1734412--1734455 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1734402 CACTCTCTCA
1734412 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1734434 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1734456 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1734745 original size:20 final size:20
Alignment explanation
Indices: 1734720--1734757 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1734710 CGATTCTCTC
1734720 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
1734740 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
1734758 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:1734949 original size:25 final size:24
Alignment explanation
Indices: 1734895--1734949 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1734885 TGTTTATTAT
* *
1734895 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1734919 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1734945 TGTTT
1 TGTTT
1734950 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1736099 original size:18 final size:18
Alignment explanation
Indices: 1736078--1736122 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1736068 TCCACTTCGG
*
1736078 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1736096 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1736114 GAGCCATCA
1 GAGCCATCA
1736123 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1736629 original size:20 final size:20
Alignment explanation
Indices: 1736604--1736649 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1736594 TAGTTTACTT
1736604 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
** * *
1736624 TCGCAACGTGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1736644 TCGCAA
1 TCGCAA
1736650 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1736658 original size:19 final size:19
Alignment explanation
Indices: 1736615--1736659 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
1736605 CGCAACACGA
1736615 AAATGACTATCGCAACGTGG
1 AAATGACTATCGCAAC-TGG
*
1736635 AAATGGCTATCGCAA-TGCG
1 AAATGACTATCGCAACTG-G
1736654 AAATGA
1 AAATGA
1736660 AAATCACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 6 0.27
20 14 0.64
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (19 bp):
AAATGACTATCGCAACTGG
Found at i:1736697 original size:18 final size:19
Alignment explanation
Indices: 1736673--1736724 Score: 79
Period size: 18 Copynumber: 2.8 Consensus size: 19
1736663 TCACAACGAC
*
1736673 AAAATCGCAATGTGAAATG
1 AAAATCGCAATGCGAAATG
*
1736692 -AAATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
1736710 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
1736725 TTTGTGTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.15
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:1736716 original size:19 final size:19
Alignment explanation
Indices: 1736643--1736724 Score: 86
Period size: 19 Copynumber: 4.6 Consensus size: 19
1736633 GGAAATGGCT
1736643 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1736662 ATCACAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
1736676 ATCGCAATGTGAAATG-AA
1 ATCGCAATGCGAAATGAAA
*
1736694 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1736713 ATCGCAATGCGA
1 ATCGCAATGCGA
1736725 TTTGTGTTTC
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
14 9 0.18
15 1 0.02
16 1 0.02
17 2 0.04
18 17 0.35
19 19 0.39
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1736794 original size:19 final size:19
Alignment explanation
Indices: 1736731--1736851 Score: 101
Period size: 20 Copynumber: 6.6 Consensus size: 19
1736721 GCGATTTGTG
1736731 TTTCGCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTCA
1736749 TTTCGCGTTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
1736765 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
1736782 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
**
1736801 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
*
1736821 TTTCGCGTTGCGATTTTAA
1 TTTCGCGTTGCGATTTTCA
*
1736840 GTTTCGTGTTGC
1 -TTTCGCGTTGC
1736852 AAAAGTAAAC
Statistics
Matches: 84, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 16 0.19
19 26 0.31
20 27 0.32
ACGTcount: A:0.12, C:0.21, G:0.24, T:0.43
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:1736851 original size:39 final size:37
Alignment explanation
Indices: 1736720--1736851 Score: 107
Period size: 39 Copynumber: 3.6 Consensus size: 37
1736710 AAAATCGCAA
1736720 TGCGATTTGT-GTTTCGCGTTGCGATTTCATTTCGCGT
1 TGCGATTT-TAGTTTCGCGTTGCGATTTCATTTCGCGT
*
1736757 TGCGATTTT-G--T--CGTTGCGATTTTCATTTCGCAT
1 TGCGATTTTAGTTTCGCGTTGCGA-TTTCATTTCGCGT
*** *
1736790 TGCGATAGCCA-TTTCCGCGTTGCGATAGTCATTTCGCGT
1 TGCGAT-TTTAGTTT-CGCGTTGCGAT-TTCATTTCGCGT
*
1736829 TGCGATTTTAAGTTTCGTGTTGC
1 TGCGATTTT-AGTTTCGCGTTGC
1736852 AAAAGTAAAC
Statistics
Matches: 74, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
32 8 0.11
33 18 0.24
34 1 0.01
36 3 0.04
37 8 0.11
38 1 0.01
39 32 0.43
40 3 0.04
ACGTcount: A:0.12, C:0.20, G:0.25, T:0.43
Consensus pattern (37 bp):
TGCGATTTTAGTTTCGCGTTGCGATTTCATTTCGCGT
Found at i:1738030 original size:14 final size:14
Alignment explanation
Indices: 1738011--1738046 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1738001 ATTGTTTAAT
1738011 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1738025 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1738039 TGATTTGT
1 TGATTTGT
1738047 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1738173 original size:14 final size:16
Alignment explanation
Indices: 1738154--1738226 Score: 64
Period size: 19 Copynumber: 4.4 Consensus size: 16
1738144 CGAAATGGCT
1738154 ATCGCAACG-A-GAAA
1 ATCGCAACGAATGAAA
1738168 ATCGCAATACGAAATGAAA
1 ATCGC-A-ACG-AATGAAA
1738187 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG-AATGAAA
1738206 ATCGCAACG-A-GAAA
1 ATCGCAACGAATGAAA
1738220 ATCGCAA
1 ATCGCAA
1738227 TGCGATTTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
14 16 0.31
15 2 0.04
16 3 0.06
17 3 0.06
18 2 0.04
19 26 0.50
ACGTcount: A:0.49, C:0.19, G:0.19, T:0.12
Consensus pattern (16 bp):
ATCGCAACGAATGAAA
Found at i:1738186 original size:19 final size:19
Alignment explanation
Indices: 1738164--1738212 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
1738154 ATCGCAACGA
1738164 GAAAATCGCAATACGAAAT
1 GAAAATCGCAATACGAAAT
*
1738183 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATACGAAAT
1738202 GAAAATCGCAA
1 GAAAATCGCAA
1738213 CGAGAAAATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATACGAAAT
Found at i:1738219 original size:19 final size:18
Alignment explanation
Indices: 1738164--1738219 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
1738154 ATCGCAACGA
*
1738164 GAAAATCGCAATACGAAAT
1 GAAAATCGCAAGA-GAAAT
*
1738183 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAA-GAGAAAT
1738202 GAAAATCGCAACGAGAAA
1 GAAAATCGCAA-GAGAAA
1738220 ATCGCAATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.52, C:0.16, G:0.20, T:0.12
Consensus pattern (18 bp):
GAAAATCGCAAGAGAAAT
Found at i:1738275 original size:20 final size:20
Alignment explanation
Indices: 1738250--1738307 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
1738240 TCGCATTGCG
*
1738250 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1738270 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
1738290 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
1738308 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1739391 original size:24 final size:24
Alignment explanation
Indices: 1739364--1739417 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1739354 GTATTCGAAA
* *
1739364 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1739388 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1739412 TTTGAT
1 TTTGAT
1739418 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:1739608 original size:12 final size:12
Alignment explanation
Indices: 1739591--1739615 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1739581 ATATAATCCT
1739591 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1739603 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1739615 G
1 G
1739616 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1741614 original size:19 final size:19
Alignment explanation
Indices: 1741592--1741722 Score: 76
Period size: 19 Copynumber: 7.7 Consensus size: 19
1741582 GGAAATTACT
*
1741592 ATCGCAATGCGAAATAAAA
1 ATCGCAATGCGAAATGAAA
*
1741611 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1741625 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
1741644 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
* *
1741658 TTCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
1741677 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
1741691 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1741710 ATCGCAACGCGAA
1 ATCGCAATGCGAA
1741723 TTTAATTTCG
Statistics
Matches: 83, Mismatches: 14, Indels: 30
0.65 0.11 0.24
Matches are distributed among these distances:
14 26 0.31
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.47
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1741634 original size:33 final size:33
Alignment explanation
Indices: 1741592--1741718 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
1741582 GGAAATTACT
*
1741592 ATCGCAATGCGAAATAAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
1741625 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1741657 TTTCGCAATACGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1741691 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1741719 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
32 1 0.01
33 80 0.98
34 1 0.01
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1741699 original size:66 final size:66
Alignment explanation
Indices: 1741593--1741725 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
1741583 GAAATTACTA
* *
1741593 TCGCAATGCGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATACGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1741658 T
66 T
* *
1741659 TCGCAATACGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATACGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1741724 T
66 T
1741725 T
1 T
1741726 AATTTCGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.17
Consensus pattern (66 bp):
TCGCAATACGAAATAAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:1741740 original size:19 final size:20
Alignment explanation
Indices: 1741718--1741760 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1741708 AAATCGCAAC
1741718 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
1741737 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
1741757 GCGA
1 GCGA
1741761 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:1741745 original size:14 final size:14
Alignment explanation
Indices: 1741746--1741779 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1741736 TGCGATTTTC
1741746 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
1741760 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
1741774 ATTTTC
1 ATTTTC
1741780 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:1741922 original size:14 final size:14
Alignment explanation
Indices: 1741903--1741937 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
1741893 TCAATTAAAG
1741903 AAATCAACTTTTAC
1 AAATCAACTTTTAC
*
1741917 AAATCACCTTTTAC
1 AAATCAACTTTTAC
1741931 AAATCAA
1 AAATCAA
1741938 TTAAACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:1744098 original size:14 final size:14
Alignment explanation
Indices: 1744079--1744115 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1744069 GGAAATGACT
*
1744079 ATCGCAACGATAGA
1 ATCGCAACGAGAGA
1744093 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1744107 ATCGCAACG
1 ATCGCAACG
1744116 CGAAATGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.41, C:0.24, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1744143 original size:47 final size:48
Alignment explanation
Indices: 1744055--1744148 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 48
1744045 ACGAGATAAT
* * *
1744055 GAGAATCGCAACGCGGAAATGACTATCGCAACGATAGAATCGCAACGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACGA
*
1744103 GAGAATCGCAACGC-GAAATGACTATCGCGACCAGACAATCGCAACG
1 GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACG
1744149 CGAAATGAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 28 0.67
48 14 0.33
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (48 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAACCAGACAATCGCAACGA
Found at i:1744161 original size:19 final size:19
Alignment explanation
Indices: 1744139--1744209 Score: 115
Period size: 19 Copynumber: 3.7 Consensus size: 19
1744129 GCGACCAGAC
1744139 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1744158 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATGAA
1744178 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1744197 AATCGCAATGCGA
1 AATCGCAACGCGA
1744210 TTTTTGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 30 0.62
20 18 0.38
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1744163 original size:33 final size:33
Alignment explanation
Indices: 1744092--1744204 Score: 109
Period size: 33 Copynumber: 3.2 Consensus size: 33
1744082 GCAACGATAG
* * *
1744092 AATCGCAACGAGAGAATCGCAACGCGAAATGAC
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
* *
1744125 TATCGCGACCAGACAATCGCAACGCGAAATGAA
1 AATCGCAACCAGACAATCGCAACGCGAAATGAA
* *
1744158 AATCGCAACCGCGAAATAAAAATCGCAACGCGAAATGAA
1 AATCGCAA-C-C---A-GACAATCGCAACGCGAAATGAA
1744197 AATCGCAA
1 AATCGCAA
1744205 TGCGATTTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
33 34 0.52
34 1 0.02
35 1 0.02
38 1 0.02
39 28 0.43
ACGTcount: A:0.44, C:0.25, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACCAGACAATCGCAACGCGAAATGAA
Found at i:1744172 original size:20 final size:19
Alignment explanation
Indices: 1744030--1744209 Score: 120
Period size: 20 Copynumber: 10.1 Consensus size: 19
1744020 TCTTTTGGTT
*
1744030 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1744049 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1744069 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1744087 G--AT-AGAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1744101 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1744117 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1744135 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1744150 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
1744170 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1744189 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1744208 GA
1 GA
1744210 TTTTTGTTTC
Statistics
Matches: 132, Mismatches: 15, Indels: 28
0.75 0.09 0.16
Matches are distributed among these distances:
14 31 0.23
15 4 0.03
16 2 0.02
17 1 0.01
18 4 0.03
19 43 0.33
20 45 0.34
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1744241 original size:19 final size:19
Alignment explanation
Indices: 1744205--1744249 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1744195 AAAATCGCAA
*
1744205 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1744224 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
1744243 TGCGATT
1 TGCGATT
1744250 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1744827 original size:20 final size:20
Alignment explanation
Indices: 1744802--1744854 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1744792 TCGCTATGTA
1744802 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
1744822 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
1744842 TATCTCGTTGCGA
1 AATCGCGTTGCGA
1744855 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:1744892 original size:20 final size:20
Alignment explanation
Indices: 1744863--1744916 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
1744853 GATTTTGTAT
1744863 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* *
1744883 TATCGTATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
1744903 TATCGCATTGCGAT
1 TATCGCATTGCGAT
1744917 TTTCCCAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:1744935 original size:61 final size:61
Alignment explanation
Indices: 1744803--1744935 Score: 142
Period size: 61 Copynumber: 2.2 Consensus size: 61
1744793 CGCTATGTAA
* * * * ** *
1744803 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * * * *
1744864 ATCGCATTGCGATAGTAAGTATCGTATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
1744926 -TCGCGTTGCG
1 ATCGCGTTGCG
1744936 TTTTACTTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
61 56 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1745027 original size:21 final size:21
Alignment explanation
Indices: 1744987--1745027 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1744977 ACTGTATACA
**
1744987 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1745008 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1745028 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1752380 original size:17 final size:17
Alignment explanation
Indices: 1752358--1752398 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
1752348 ATGGTTTTTA
1752358 GAACCGGACCGGTCAGT
1 GAACCGGACCGGTCAGT
**
1752375 GAACCGGTTCGGTCAGT
1 GAACCGGACCGGTCAGT
1752392 GAACCGG
1 GAACCGG
1752399 TAGTGCTACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.22, C:0.27, G:0.37, T:0.15
Consensus pattern (17 bp):
GAACCGGACCGGTCAGT
Found at i:1752399 original size:17 final size:17
Alignment explanation
Indices: 1752367--1752399 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1752357 AGAACCGGAC
1752367 CGGTCAGTGAACCGGTT
1 CGGTCAGTGAACCGGTT
1752384 CGGTCAGTGAACCGGT
1 CGGTCAGTGAACCGGT
1752400 AGTGCTACCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.24, G:0.36, T:0.21
Consensus pattern (17 bp):
CGGTCAGTGAACCGGTT
Found at i:1752522 original size:21 final size:22
Alignment explanation
Indices: 1752486--1752526 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1752476 TAAGAAATTA
1752486 AATAAAAATACCAAAAACATTT
1 AATAAAAATACCAAAAACATTT
*
1752508 AATAAAAA-ACTAAAAACAT
1 AATAAAAATACCAAAAACAT
1752527 CCCCACACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (22 bp):
AATAAAAATACCAAAAACATTT
Found at i:1755154 original size:17 final size:17
Alignment explanation
Indices: 1755124--1755213 Score: 69
Period size: 17 Copynumber: 5.2 Consensus size: 17
1755114 TGATCGGGTT
* * *
1755124 TTATATTTTTTTTATCA
1 TTATAATTTATTTATTA
1755141 TTATAATTTATTTATTA
1 TTATAATTTATTTATTA
*
1755158 TTATTA-TTATTATTATTA
1 TTATAATTTA-T-TTATTA
1755176 TTATATATTT-TTTATTA
1 TTATA-ATTTATTTATTA
* *
1755193 TTAATAA-TAATTTATAA
1 TT-ATAATTTATTTATTA
1755210 TTAT
1 TTAT
1755214 TTTGTAGGTC
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
16 6 0.10
17 37 0.62
18 14 0.23
19 1 0.02
20 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATAATTTATTTATTA
Found at i:1755160 original size:3 final size:3
Alignment explanation
Indices: 1755152--1755195 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
1755142 TATAATTTAT
1755152 TTA TTA TTA TTA TTA TTA TTA TTA TTA TATA TT- TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
1755196 ATAATAATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.10
3 32 0.82
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1755185 original size:32 final size:32
Alignment explanation
Indices: 1755135--1755195 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1755125 TATATTTTTT
*
1755135 TTATCATTATAATTTATTTATTATTATTATTA
1 TTATCATTATAATATATTTATTATTATTATTA
* * *
1755167 TTATTATTATTATATATTTTTTATTATTA
1 TTATCATTATAATATATTTATTATTATTA
1755196 ATAATAATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (32 bp):
TTATCATTATAATATATTTATTATTATTATTA
Found at i:1759984 original size:98 final size:98
Alignment explanation
Indices: 1759810--1760592 Score: 1073
Period size: 98 Copynumber: 7.8 Consensus size: 98
1759800 CAACTTCACA
* * *
1759810 GCGGCTGACTGTCAACAAATATTTTCAGAGCCAATTTTAACTTCACAGCGAATGATATTGGACTC
1 GCGGCTGACTGTCAACAAACATTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* *
1759875 GAGACAACACAAGCTCAACATCATAGCGAAGGG
66 GAGACAACACAAGCTCAACTTCACAGCGAAGGG
*
1759908 GCGGCTGACTGTCAACAAACATTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGGCTC
1 GCGGCTGACTGTCAACAAACATTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
*
1759973 GAGACAGCACAAGCTCAACTTCACAGCGAAGGG
66 GAGACAACACAAGCTCAACTTCACAGCGAAGGG
* * * **
1760006 GAGACTGACTATCAACAAACATTTTCAGAGTAAATTTCAACTTCACAGCGAAGGATATTGGACTC
1 GCGGCTGACTGTCAACAAACATTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
*
1760071 GAGACAGCACAAGCTCAACTTCACAGCGAAGGG
66 GAGACAACACAAGCTCAACTTCACAGCGAAGGG
*
1760104 GCGGCTGACTGTCAACAAACATTTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTC
1 GCGGCTGACTGTCAACAAACATTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
*
1760169 GAGACAACACAAGCTCAACTTCACAGTGAAGGG
66 GAGACAACACAAGCTCAACTTCACAGCGAAGGG
* * *
1760202 GCGGCTGACTGTCAACAAACATATTCAGAGTCAATTTTAACTTCACAGCGAAGGATATTGGACTC
1 GCGGCTGACTGTCAACAAACATTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
* *
1760267 GAGACAGCACAAGCTCAACTTCACAGTGAAGGG
66 GAGACAACACAAGCTCAACTTCACAGCGAAGGG
* * * *
1760300 GCGGCTGACTGTCAACAAACATATTCAGAGTCAATTTCAACTTCACAACGAAGAATATTGGACTC
1 GCGGCTGACTGTCAACAAACATTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
*
1760365 GAGATAACACAAGCTCAACTTCACAGCGAAGGG
66 GAGACAACACAAGCTCAACTTCACAGCGAAGGG
* *
1760398 GCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTCAAAGTCAATTTCAACTTCACAGCGAAG
1 GCGGCTGACTGTCAACAAAC-A-TTTTCAG----------AGCCAATTTCAACTTCACAGCGAAG
*
1760463 AATATTGGACTCGAGACAACACCAA-CTCAACTTCACAGCGAAGGG
54 GATATTGGACTCGAGACAACA-CAAGCTCAACTTCACAGCGAAGGG
* * *
1760508 GCGGCTGGCTGTCAACAAACAACTTTCCAGTTTTAGATCCAATTTCAACTTCACGGCGAAGGATA
1 GCGGCTGACTGTCAACAAAC-A-TTTTCAG----AG--CCAATTTCAACTTCACAGCGAAGGATA
* *
1760573 TTGGACTCGAAACAGCACAA
58 TTGGACTCGAGACAACACAA
1760593 CTTTCATTGG
Statistics
Matches: 623, Mismatches: 47, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
98 477 0.77
99 1 0.00
100 6 0.01
104 3 0.00
105 3 0.00
106 39 0.06
110 91 0.15
111 3 0.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.21
Consensus pattern (98 bp):
GCGGCTGACTGTCAACAAACATTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTC
GAGACAACACAAGCTCAACTTCACAGCGAAGGG
Found at i:1760520 original size:110 final size:108
Alignment explanation
Indices: 1760321--1760592 Score: 390
Period size: 110 Copynumber: 2.5 Consensus size: 108
1760311 TCAACAAACA
* *
1760321 TATTCAGAGTCAATTTCAACTTCACAACGAAGAATATTGGACTCGAGATAACACAAGCTCAACTT
1 TATTCAGAGTCAATTTCAACTTCACAGCGAAGAATATTGGACTCGAGACAACACAAGCTCAACTT
*
1760386 CACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTT
66 CACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTCCAG-T
*
1760430 TCATTCAAAGTCAATTTCAACTTCACAGCGAAGAATATTGGACTCGAGACAACACCAA-CTCAAC
1 T-ATTCAGAGTCAATTTCAACTTCACAGCGAAGAATATTGGACTCGAGACAACA-CAAGCTCAAC
* *
1760494 TTCACAGCGAAGGGGCGGCTGGCTGTCAACAAACAACTTTCCAGT
64 TTCACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTCCAGT
* * * *
1760539 T-TT-AGA-TCCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAAACAGCACAA
1 TATTCAGAGT-CAATTTCAACTTCACAGCGAAGAATATTGGACTCGAGACAACACAA
1760593 CTTTCATTGG
Statistics
Matches: 149, Mismatches: 11, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
105 4 0.03
106 41 0.28
107 2 0.01
109 3 0.02
110 96 0.64
111 3 0.02
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (108 bp):
TATTCAGAGTCAATTTCAACTTCACAGCGAAGAATATTGGACTCGAGACAACACAAGCTCAACTT
CACAGCGAAGGGGCGACTGACTGTCAACAAACAACTTTCCAGT
Found at i:1760854 original size:84 final size:82
Alignment explanation
Indices: 1760701--1760888 Score: 259
Period size: 84 Copynumber: 2.3 Consensus size: 82
1760691 AATCGTGTCC
* * **
1760701 ACCAAATACCTTCGAGTTCGACTACGCTTAGATCCAAGGCATCATTTGCAGTATAACTTAAGTCG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGATCCAAGGCATCATTTGCAACATAACTTAAGTCG
* *
1760766 AGAAGTGTTATCTGCCA
66 AGAAGGGCTATCTGCCA
* * *
1760783 ACCAGAGACCTTCGAGTTTGACTACGCTCAGCTCCAAGGCACATCATTTGCAACATAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGATCCAAGG--CATCATTTGCAACATAACTTAAGT
1760848 CGAGAAGGGCTATCTGCCA
64 CGAGAAGGGCTATCTGCCA
*
1760867 ACCAAAGACCTGACGAGTTCGA
1 ACCAAAGACCT-TCGAGTTCGA
1760889 TTTCATTCAG
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
82 34 0.37
84 49 0.54
85 8 0.09
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.24
Consensus pattern (82 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGATCCAAGGCATCATTTGCAACATAACTTAAGTCG
AGAAGGGCTATCTGCCA
Found at i:1761150 original size:3 final size:3
Alignment explanation
Indices: 1761110--1761179 Score: 59
Period size: 3 Copynumber: 21.7 Consensus size: 3
1761100 CCGGGTTTTA
* * * *
1761110 TAT TTT TAT TTT TAT CAT TAT AATT TATT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT
1761158 TAT TAT ATATT TAT TAT TAT TA
1 TAT TAT -TA-T TAT TAT TAT TA
1761180 ATAATAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
3 41 0.73
4 14 0.25
5 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1761152 original size:33 final size:32
Alignment explanation
Indices: 1761110--1761179 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
1761100 CCGGGTTTTA
* *
1761110 TATTTTTATTTTTATCATTATA-ATTTATTTATT
1 TATTATTATTATTATCATTATATATTTA-TTA-T
*
1761143 TATTATTATTATTATTATTATATATTTATTAT
1 TATTATTATTATTATCATTATATATTTATTAT
1761175 TATTA
1 TATTA
1761180 ATAATAATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 6 0.18
33 22 0.67
34 5 0.15
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (32 bp):
TATTATTATTATTATCATTATATATTTATTAT
Found at i:1761154 original size:17 final size:17
Alignment explanation
Indices: 1761120--1761179 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 17
1761110 TATTTTTATT
* *
1761120 TTTATCATTATAATTTA
1 TTTATTATTATTATTTA
1761137 TTTA-T-TTATTA-TTA
1 TTTATTATTATTATTTA
*
1761151 -TTATTATTATTATATA
1 TTTATTATTATTATTTA
1761167 TTTATTATTATTA
1 TTTATTATTATTA
1761180 ATAATAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 3 0.08
14 4 0.11
15 11 0.31
16 2 0.06
17 16 0.44
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTATTATTATTATTTA
Found at i:1761178 original size:20 final size:20
Alignment explanation
Indices: 1761107--1761198 Score: 74
Period size: 20 Copynumber: 5.0 Consensus size: 20
1761097 TGACCGGGTT
* * *
1761107 TTATATTTTTATTTTTATCA
1 TTATATATTTATTATTATTA
1761127 TTATA-ATTTA-T-TTA-T-
1 TTATATATTTATTATTATTA
1761142 TTAT-TA-TTATTATTATTA
1 TTATATATTTATTATTATTA
1761160 TTATATATTTATTATTATTA
1 TTATATATTTATTATTATTA
* *
1761180 ATA-ATAATTTATAATTATT
1 TTATAT-ATTTATTATTATT
1761199 TTGTAGGTCC
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
14 3 0.05
15 6 0.10
16 3 0.05
17 4 0.07
18 5 0.08
19 8 0.13
20 31 0.52
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (20 bp):
TTATATATTTATTATTATTA
Found at i:1761193 original size:10 final size:10
Alignment explanation
Indices: 1761127--1761199 Score: 51
Period size: 10 Copynumber: 7.2 Consensus size: 10
1761117 ATTTTTATCA
1761127 TTATAATTTAT
1 TTATAA-TTAT
*
1761138 TTATTTATTA-
1 TTA-TAATTAT
*
1761148 TTATTATTA-
1 TTATAATTAT
*
1761157 TTATTATATAT
1 TTATAAT-TAT
*
1761168 TTATTATTAT
1 TTATAATTAT
* *
1761178 TAATAATAAT
1 TTATAATTAT
1761188 TTATAATTAT
1 TTATAATTAT
1761198 TT
1 TT
1761200 TGTAGGTCCC
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
9 13 0.25
10 25 0.47
11 13 0.25
12 2 0.04
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTATAATTAT
Found at i:1764510 original size:16 final size:16
Alignment explanation
Indices: 1764489--1764520 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1764479 TACTTGGCGG
1764489 GAAAGTAAGTGAATAA
1 GAAAGTAAGTGAATAA
1764505 GAAAGTAAGTGAATAA
1 GAAAGTAAGTGAATAA
1764521 AATAAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.19
Consensus pattern (16 bp):
GAAAGTAAGTGAATAA
Found at i:1764888 original size:2 final size:2
Alignment explanation
Indices: 1764881--1764907 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1764871 ATTAAAGTAA
1764881 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1764908 CTTAGGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1775588 original size:2 final size:2
Alignment explanation
Indices: 1775581--1775616 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1775571 GACTGAATTG
1775581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1775617 TGAGATTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1790142 original size:60 final size:59
Alignment explanation
Indices: 1790058--1790215 Score: 167
Period size: 59 Copynumber: 2.7 Consensus size: 59
1790048 AACTTTGTTG
*
1790058 AATTATTTAGAATTAGGACAAAATTGATAGCATTAT-TAAATGCGATGGTTAAAATTTTCA
1 AATTATTTAGAATTAGGACAAAATTGATAGAATT-TGTAAATGCGA-GGTTAAAATTTTCA
* * ** * **
1790118 AATTATTTAGGATTGGGATTAAATTGATAGAATTTGTAAATGTGAGGTT-AAATTATTTG
1 AATTATTTAGAATTAGGACAAAATTGATAGAATTTGTAAATGCGAGGTTAAAATT-TTCA
* ** *
1790177 AATTATTTAAAATTAAAACTAAATTGATAGAATTTGTAA
1 AATTATTTAGAATTAGGACAAAATTGATAGAATTTGTAA
1790216 GTACCAAGGA
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
58 5 0.06
59 40 0.49
60 37 0.45
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (59 bp):
AATTATTTAGAATTAGGACAAAATTGATAGAATTTGTAAATGCGAGGTTAAAATTTTCA
Found at i:1794841 original size:156 final size:158
Alignment explanation
Indices: 1794535--1795220 Score: 843
Period size: 156 Copynumber: 4.4 Consensus size: 158
1794525 GTATTATATT
* * * * *
1794535 ATGGTATATGAGCATGCGGTTCAAATTTAGTAAAAACGAACTTAAAAT-AAGGATGAATTGAAGA
1 ATGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAACGAACTTAAAATAAAGGATGAATTGAAGA
* * * *
1794599 AAT-AAGAAAATTATGAAAAA-TTGA--GA-GAAATTGAAAAATAGAAAT---TTTGTTATCAAA
66 AATAAAG-AAATTATAAAAAATTTGAGGGACTAAATTG-AAAATA-AAATAAAATTATTATCAAA
1794656 AAGAGGAATTGAAAGTACATATGTATTCTA-
128 AAGAGGAATTGAAAGTACATATGTATTCTAG
*
1794686 A-GGTTTAGGAGCATGTGATTCAAATTTGGTAATAACGAACTTAAAATAAAGGATGAATTGGAA-
1 ATGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAACGAACTTAAAATAAAGGATGAATT-GAAG
*
1794749 AAATAAAGAAATTATAAAAAATTTGAGGGACTAAATTGAAAATAAAATAAAATAATTATCAAAAA
65 AAATAAAGAAATTATAAAAAATTTGAGGGACTAAATTGAAAATAAAATAAAATTATTATCAAAAA
*
1794814 GAGGAATTGAAAGTACATACGTATTCTA-
130 GAGGAATTGAAAGTACATATGTATTCTAG
* *
1794842 A-GGTTTAGGAGCATGTGATTCAAATTTGGTAATAACGAACTTAAAATAAAGGATAAATTAGAA-
1 ATGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAACGAACTTAAAATAAAGGATGAATT-GAAG
1794905 AAATAAAGAAATTATAAAAAATTTGAGGGACTAAATTGAAAATAAAATAAAATTATTATCAAAAA
65 AAATAAAGAAATTATAAAAAATTTGAGGGACTAAATTGAAAATAAAATAAAATTATTATCAAAAA
*
1794970 GAGTAATTGAAAGTACATATGTATTCTACG
130 GAGGAATTGAAAGTACATATGTATTCTA-G
* * * * * * * *
1795000 ATGGTTTGGGAGTATGTAATTCAAATTTGATAAAAATTGTATTTTAAATAAAGGATGAATTGAAG
1 ATGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAA-CGAACTTAAAATAAAGGATGAATTGAAG
* * * * * *
1795065 AAATAAGGAAATTATAAAAAAATT-AGGGACTCAATTG-AAA-AATATAAAACTTGTTACCAAAA
65 AAATAAAGAAATTATAAAAAATTTGAGGGACTAAATTGAAAATAAAATAAAA-TTATTATCAAAA
*
1795127 AGAGGAATTGAAAGTACATATGTATTATAAG
129 AGAGGAATTGAAAGTACATATGTATTCT-AG
* * * *
1795158 ATGGTTTAGGAGTATATGGTTCAAATTTGGTAAAAAC-ATACTTAAAATAGAGGATGAATTGAA
1 ATGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAACGA-ACTTAAAATAAAGGATGAATTGAA
1795221 TGAATAATGA
Statistics
Matches: 472, Mismatches: 45, Indels: 30
0.86 0.08 0.05
Matches are distributed among these distances:
150 40 0.08
151 28 0.06
152 10 0.02
153 4 0.01
154 8 0.02
155 6 0.01
156 189 0.40
157 29 0.06
158 72 0.15
159 45 0.10
160 41 0.09
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (158 bp):
ATGGTTTAGGAGCATGTGATTCAAATTTGGTAAAAACGAACTTAAAATAAAGGATGAATTGAAGA
AATAAAGAAATTATAAAAAATTTGAGGGACTAAATTGAAAATAAAATAAAATTATTATCAAAAAG
AGGAATTGAAAGTACATATGTATTCTAG
Found at i:1795203 original size:317 final size:307
Alignment explanation
Indices: 1794552--1795220 Score: 827
Period size: 317 Copynumber: 2.1 Consensus size: 307
1794542 ATGAGCATGC
* *
1794552 GGTTCAAATTTAGTAAAAACGAACTTAAAAT-AAGGATGAATTGAAGAAATAAGAAAATTATGAA
1 GGTTCAAATTTGGTAAAAACGAACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATTATAAA
* *
1794616 AAATTGAGAGAAATTGAAAAATAGAAATTTTGTTATCAAAAAGAGGAATTGAAAGTACATATGTA
66 AAATTGAGAGAAATTGAAAAATAGAAATATTATTATCAAAAAGAGGAATTGAAAGTACATATGTA
* * *
1794681 TTCTAAGGTTTAGGAGCATGTGATTCAAATTTGGTAATAACGAACTTAAAATAAAGGATGAATTG
131 TTCTAAGGTTTAGGAGCATGTAATTCAAATTTGATAAAAACGAACTTAAAATAAAGGATGAATTG
* *
1794746 GAAAAATAAAGAAATTATAAAAAATTTGAGGGACTAAATTGAAAATAAAATAAAATAATTATCAA
196 GAAAAATAAAGAAATTATAAAAAAATTGAGGGACTAAATTGAAAATAAAATAAAATAATTACCAA
* *
1794811 AAAGAGGAATTGAAAGTACATACGTATTCTAAGGTTTAGGAGCATGT
261 AAAGAGGAATTGAAAGTACATACGTATTATAAGGTTTAGGAGCATAT
* * *
1794858 GATTCAAATTTGGTAATAACGAACTTAAAATAAAGGATAAATTAGAA-AAATAA-AGAAATTATA
1 GGTTCAAATTTGGTAAAAACGAACTTAAAATAAAGGATGAATT-GAAGAAATAAGA-AAATTATA
* *
1794921 AAAAATTTGAGGGACTAAATTG-AAAATA-AAATAAAATTATTATCAAAAAGAGTAATTGAAAGT
64 AAAAA-TTGA--GA-GAAATTGAAAAATAGAAAT---ATTATTATCAAAAAGAGGAATTGAAAGT
* * * * * *
1794984 ACATATGTATTCTACGATGGTTTGGGAGTATGTAATTCAAATTTGATAAAAATTGTATTTTAAAT
122 ACATATGTATTCTA--A-GGTTTAGGAGCATGTAATTCAAATTTGATAAAAA-CGAACTTAAAAT
* * *
1795049 AAAGGATGAATT-GAAGAAATAAGGAAATTATAAAAAAATT-AGGGACTCAATTG-AAA-AATAT
183 AAAGGATGAATTGGAA-AAATAAAGAAATTATAAAAAAATTGAGGGACTAAATTGAAAATAAAAT
** * *
1795110 AAAACTTGTTACCAAAAAGAGGAATTGAAAGTACATATGTATTATAAGATGGTTTAGGAGTATAT
247 AAAA-TAATTACCAAAAAGAGGAATTGAAAGTACATACGTATTAT-A-A-GGTTTAGGAGCATAT
*
1795175 GGTTCAAATTTGGTAAAAAC-ATACTTAAAATAGAGGATGAATTGAA
1 GGTTCAAATTTGGTAAAAACGA-ACTTAAAATAAAGGATGAATTGAA
1795221 TGAATAATGA
Statistics
Matches: 310, Mismatches: 33, Indels: 30
0.83 0.09 0.08
Matches are distributed among these distances:
306 29 0.09
307 28 0.09
308 7 0.02
309 4 0.01
310 8 0.03
311 6 0.02
312 39 0.13
313 8 0.03
314 39 0.13
315 45 0.15
316 47 0.15
317 50 0.16
ACGTcount: A:0.49, C:0.05, G:0.17, T:0.29
Consensus pattern (307 bp):
GGTTCAAATTTGGTAAAAACGAACTTAAAATAAAGGATGAATTGAAGAAATAAGAAAATTATAAA
AAATTGAGAGAAATTGAAAAATAGAAATATTATTATCAAAAAGAGGAATTGAAAGTACATATGTA
TTCTAAGGTTTAGGAGCATGTAATTCAAATTTGATAAAAACGAACTTAAAATAAAGGATGAATTG
GAAAAATAAAGAAATTATAAAAAAATTGAGGGACTAAATTGAAAATAAAATAAAATAATTACCAA
AAAGAGGAATTGAAAGTACATACGTATTATAAGGTTTAGGAGCATAT
Found at i:1795307 original size:8 final size:8
Alignment explanation
Indices: 1795296--1795326 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1795286 TTTTTTGAGT
*
1795296 ATTTCGAA
1 ATTTCAAA
1795304 ATTTCAAA
1 ATTTCAAA
1795312 ATTTCAAA
1 ATTTCAAA
1795320 ATTTCAA
1 ATTTCAA
1795327 CCCCACTCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (8 bp):
ATTTCAAA
Found at i:1804966 original size:2 final size:2
Alignment explanation
Indices: 1804959--1804986 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1804949 AAAGTGGGAA
1804959 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1804987 GGTTAATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1805342 original size:117 final size:117
Alignment explanation
Indices: 1805221--1805458 Score: 413
Period size: 117 Copynumber: 2.0 Consensus size: 117
1805211 AACAACTGAT
* *
1805221 AAAATAATTTAATCACTCAATGATTTACTCTAAATTTGTTCATATTCATTGATTGATTTGTGCTT
1 AAAATAATTCAATCACTCAATGATTTACGCTAAATTTGTTCATATTCATTGATTGATTTGTGCTT
* *
1805286 TATGAATCCCTACCACTTTCAAGAATAGCAAAGCTTCAATGCTTAATCTTCC
66 TATGAATCCCTACCACTTTCAAGAATAACAAAGCTTCAATGCATAATCTTCC
* *
1805338 AAAATAATTCCATTACTCAATGATTTACGCTAAATTTGTTCATATTCATTGATTGATTTGTGCTT
1 AAAATAATTCAATCACTCAATGATTTACGCTAAATTTGTTCATATTCATTGATTGATTTGTGCTT
*
1805403 TATGAATCTCTACCACTTTCAAGAATAACAAAGCTTCAATGCATAATCTTCC
66 TATGAATCCCTACCACTTTCAAGAATAACAAAGCTTCAATGCATAATCTTCC
1805455 AAAA
1 AAAA
1805459 GTATTTAGGA
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 114 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.38
Consensus pattern (117 bp):
AAAATAATTCAATCACTCAATGATTTACGCTAAATTTGTTCATATTCATTGATTGATTTGTGCTT
TATGAATCCCTACCACTTTCAAGAATAACAAAGCTTCAATGCATAATCTTCC
Found at i:1805776 original size:14 final size:14
Alignment explanation
Indices: 1805757--1805787 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1805747 ATCGGGAATT
*
1805757 TTTATTTTTTATTA
1 TTTATTTTATATTA
1805771 TTTATTTTATATTA
1 TTTATTTTATATTA
1805785 TTT
1 TTT
1805788 GTATATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATATTA
Found at i:1808080 original size:11 final size:11
Alignment explanation
Indices: 1808064--1808094 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1808054 TTTTTTATCC
*
1808064 AAAAAAATAAA
1 AAAAAAACAAA
1808075 AAAAAAACAAA
1 AAAAAAACAAA
1808086 AAAAAAACA
1 AAAAAAACA
1808095 TCATCCCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.90, C:0.06, G:0.00, T:0.03
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:1813678 original size:15 final size:15
Alignment explanation
Indices: 1813654--1813691 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1813644 CGCCTTTGAA
*
1813654 TGATTCAGTGTTAAC
1 TGATTCAGTGCTAAC
*
1813669 TGATTTAGTGCTAAC
1 TGATTCAGTGCTAAC
1813684 TGATTCAG
1 TGATTCAG
1813692 CAAAACAGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.39
Consensus pattern (15 bp):
TGATTCAGTGCTAAC
Found at i:1814271 original size:32 final size:33
Alignment explanation
Indices: 1814235--1814310 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 33
1814225 TTTGGTTACT
*
1814235 AAATTTAATTTTAATTTAATTACT-TAACTTTC
1 AAATTTAATTTTAATTTAATCACTCTAACTTTC
* ** *
1814267 AAA-TTACTCCTAATTTGATCACTCTAACTTTC
1 AAATTTAATTTTAATTTAATCACTCTAACTTTC
*
1814299 AAATTTGATTTT
1 AAATTTAATTTT
1814311 TTATTTTTAA
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
31 15 0.45
32 14 0.42
33 4 0.12
ACGTcount: A:0.34, C:0.14, G:0.03, T:0.49
Consensus pattern (33 bp):
AAATTTAATTTTAATTTAATCACTCTAACTTTC
Found at i:1817687 original size:16 final size:18
Alignment explanation
Indices: 1817668--1817703 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1817658 ATATTAATGG
1817668 GGTAAAA-AAA-TAAAAA
1 GGTAAAAGAAATTAAAAA
1817684 GGTAAAAGAAATTAAAAA
1 GGTAAAAGAAATTAAAAA
1817702 GG
1 GG
1817704 AGTAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.14
Consensus pattern (18 bp):
GGTAAAAGAAATTAAAAA
Found at i:1817832 original size:12 final size:13
Alignment explanation
Indices: 1817812--1817851 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
1817802 CATTATATTA
1817812 AGAAAAAAATAAT
1 AGAAAAAAATAAT
1817825 AGAAAAAAATAA-
1 AGAAAAAAATAAT
*
1817837 AGTAAAAATATAAT
1 AG-AAAAAAATAAT
1817851 A
1 A
1817852 TATATAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 2 0.08
13 21 0.88
14 1 0.04
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (13 bp):
AGAAAAAAATAAT
Found at i:1817849 original size:26 final size:25
Alignment explanation
Indices: 1817814--1817880 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 25
1817804 TTATATTAAG
1817814 AAAAAAATAATAGAAAAAAATAAAGT
1 AAAAAAATAATAGAAAAAAATAAA-T
* * * *
1817840 AAAAATATAATATATATAAATAAAT
1 AAAAAAATAATAGAAAAAAATAAAT
*
1817865 AAAAACAAAAATAGAA
1 AAAAA-AATAATAGAA
1817881 TATTAAGAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
25 6 0.19
26 26 0.81
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (25 bp):
AAAAAAATAATAGAAAAAAATAAAT
Found at i:1817900 original size:17 final size:17
Alignment explanation
Indices: 1817880--1817939 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 17
1817870 CAAAAATAGA
1817880 ATATTAAGAAAAAATAT
1 ATATTAAGAAAAAATAT
* *
1817897 ATATAAAAACGTATAAAATAT
1 ATAT--TAA-G-AAAAAATAT
1817918 AATATTAAGAAAAAATAT
1 -ATATTAAGAAAAAATAT
1817936 ATAT
1 ATAT
1817940 ACATAGTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 8 0.24
18 8 0.24
19 3 0.09
20 3 0.09
21 8 0.24
22 4 0.12
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (17 bp):
ATATTAAGAAAAAATAT
Found at i:1817974 original size:2 final size:2
Alignment explanation
Indices: 1817967--1818042 Score: 120
Period size: 2 Copynumber: 38.5 Consensus size: 2
1817957 AAATTAATAC
1817967 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1818009 AT AT AT AT AT AT AT A- AT GAT AT A- AG AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT A
1818043 ATAAAAATAA
Statistics
Matches: 70, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
1 2 0.03
2 66 0.94
3 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1819556 original size:106 final size:106
Alignment explanation
Indices: 1819371--1819577 Score: 299
Period size: 106 Copynumber: 2.0 Consensus size: 106
1819361 CTGGTAATGG
* * * * *
1819371 ATATCCTTCATTGTGAAGTTGAAATTGACCCTGAAATTGGGAAGTTGTTTATTGACAGTCGGCCA
1 ATATCCTTCACTGTGAAGTTGAAATTGACCCTGAAACTGGGAAATTGTTTATTGACACTCAGCCA
*
1819436 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAATCCA
66 TCCCTTCGTTGTGAAGTTAAACTTGTGTTGTCTCGAATCCA
*** *
1819477 ATATCCTTCACTGTGAAGTTGAAATTGGTTCTGAAACTGGGAAATTGTTTGTTGACAACT-AGCC
1 ATATCCTTCACTGTGAAGTTGAAATTGACCCTGAAACTGGGAAATTGTTTATTGAC-ACTCAGCC
*
1819541 GTCCCTTCGTTGTGAAGTTAAACTTGTGTTGTCTCGA
65 ATCCCTTCGTTGTGAAGTTAAACTTGTGTTGTCTCGA
1819578 GTGGCACGAT
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
106 87 0.98
107 2 0.02
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (106 bp):
ATATCCTTCACTGTGAAGTTGAAATTGACCCTGAAACTGGGAAATTGTTTATTGACACTCAGCCA
TCCCTTCGTTGTGAAGTTAAACTTGTGTTGTCTCGAATCCA
Found at i:1820272 original size:68 final size:65
Alignment explanation
Indices: 1820190--1820334 Score: 200
Period size: 67 Copynumber: 2.2 Consensus size: 65
1820180 TGTTTTATGA
* * **
1820190 AAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAA
1 AAACTGTCTCAAGGGAAACAAAA-TCTGTTTTAAGGGAAATAAATTCAAAGA-TTT-TGTTTCAA
1820255 GAG
63 GAG
* * *
1820258 AAACTGTCTCAAGGGAGACAAAATCTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGG
1 AAACTGTCTCAAGGGAAACAAAATCTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAG
1820323 AAACTGTCTCAA
1 AAACTGTCTCAA
1820335 TAGAGACGAA
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
65 22 0.31
66 3 0.04
67 24 0.34
68 21 0.30
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.30
Consensus pattern (65 bp):
AAACTGTCTCAAGGGAAACAAAATCTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAG
Found at i:1820296 original size:67 final size:65
Alignment explanation
Indices: 1820190--1820499 Score: 212
Period size: 65 Copynumber: 4.6 Consensus size: 65
1820180 TGTTTTATGA
* * **
1820190 AAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGATTTTGTGTTTCAA
1 AAACTGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAGA-TTT-TGTTTCAA
1820255 GAG
63 GAG
* * *
1820258 AAACTGTCTCAAGGGAGACAAAATCTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGG
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAG
** * * * * *
1820323 AAACTGTCTCAATAGAGACGAAATTTGTTTCAAGAGAAACT--ATCTCAAGAGAGACAAAACTTA
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-TAAAT-TC-A-A-AG-----ATTTT
* *
1820386 GTTCCAAAAG
56 GTTTCAAGAG
* * * *** * * * *
1820396 AAATTGTCTCAAGGGAGACGAAATTTGTTTCAAATAAAACATATTCAAATAATTTT-TTTCAAGG
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAA-GATTTTGTTTCAAGA
1820460 G
65 G
* * *
1820461 AAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAA
1 AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
1820500 CTGTCTCAAG
Statistics
Matches: 190, Mismatches: 39, Indels: 29
0.74 0.15 0.11
Matches are distributed among these distances:
64 2 0.01
65 82 0.43
66 8 0.04
67 25 0.13
68 23 0.12
70 1 0.01
71 1 0.01
72 1 0.01
73 45 0.24
74 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.29
Consensus pattern (65 bp):
AAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATTTTGTTTCAAGAG
Found at i:1820362 original size:36 final size:36
Alignment explanation
Indices: 1820310--1820826 Score: 303
Period size: 36 Copynumber: 15.0 Consensus size: 36
1820300 ATTCAAAGAT
* *
1820310 TTTGTTTCAAGGGAAACTGTCTCAATAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
1820346 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * * *
1820382 CTTAGTTCCAAAAGAAATTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*** * *
1820419 TTTGTTTCAAATAAAACATAT-TC-----A-A-ATAA
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
* *
1820448 TTTTTTTCAAGGGAAACTGTCTCAAGAGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
1820484 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * *
1820520 TTTATTTCAAGGGAAA-TGTTTTC-A-A-TG-----T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
* *
1820548 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
1820585 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
1820622 TTTGTTTCAAGGGAAA-TGTTTTC-A-A-TG-----T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
* *
1820650 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
1820687 TTTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * * *
1820724 TTCGTTTCAAAGGAAA-TGTTTTC-A-A-TG-----T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
* * *
1820752 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAATAT
1 TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA-AA
* * *
1820790 TTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1820826 T
1 T
1820827 CTTCTTTTTA
Statistics
Matches: 365, Mismatches: 70, Indels: 92
0.69 0.13 0.17
Matches are distributed among these distances:
28 8 0.02
29 62 0.17
30 10 0.03
31 1 0.00
32 3 0.01
33 3 0.01
34 4 0.01
35 8 0.02
36 138 0.38
37 121 0.33
38 7 0.02
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:1820425 original size:138 final size:138
Alignment explanation
Indices: 1820256--1820515 Score: 360
Period size: 138 Copynumber: 1.9 Consensus size: 138
1820246 GTGTTTCAAG
* ** * * *
1820256 AGAAACTGTCTCAAGGGAGACAAAATCTGTTTTAGGGGAAATAAATTCAAA-GATTTTGTTTCAA
1 AGAAACTGTCTCAAGGGAGACAAAATCTGTTTCAAAGAAAACAAATTCAAATAATTTT-TTTCAA
* *
1820320 GGGAAACTGTCTCAATAGAGACGAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
65 GGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTT
1820385 AGTTCCAAA
130 AGTTCCAAA
* * * * *
1820394 AGAAATTGTCTCAAGGGAGACGAAATTTGTTTCAAATAAAACATATTCAAATAATTTTTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATCTGTTTCAAAGAAAACAAATTCAAATAATTTTTTTCAAG
* * *
1820459 GGAAACTGTCTCAAGAGAGATAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
66 GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
1820516 GAAATTTATT
Statistics
Matches: 105, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
138 100 0.95
139 5 0.05
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (138 bp):
AGAAACTGTCTCAAGGGAGACAAAATCTGTTTCAAAGAAAACAAATTCAAATAATTTTTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTA
GTTCCAAA
Found at i:1820602 original size:37 final size:37
Alignment explanation
Indices: 1820551--1820826 Score: 209
Period size: 37 Copynumber: 7.9 Consensus size: 37
1820541 TCAATGTTTA
*
1820551 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* *
1820588 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* *
1820624 TGTTTCAAGGGAAA-TGTTTTCAA---TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAATTT
*
1820652 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* *
1820690 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* * * *
1820726 CGTTTCAAAGGAAA-TGTTTTCAA---TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGGAGACAAAATTT
* *
1820754 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
* * *
1820792 TGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAAT
1820827 CTTCTTTTTA
Statistics
Matches: 186, Mismatches: 27, Indels: 52
0.70 0.10 0.20
Matches are distributed among these distances:
28 4 0.02
29 34 0.18
30 4 0.02
32 2 0.01
33 2 0.01
35 2 0.01
36 40 0.22
37 92 0.49
38 6 0.03
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:1820826 original size:102 final size:102
Alignment explanation
Indices: 1820348--1820826 Score: 658
Period size: 102 Copynumber: 4.7 Consensus size: 102
1820338 AGACGAAATT
* * * * * ** * * *
1820348 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCAAGGGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *** ** * *
1820413 ACGAAATTTGTTTCAAATAAAACATATTCAAATAATTT-
66 ACAAAATTTGTTTCAAGGGAAATGTTTTC-AAT-GTTTA
* * * *
1820451 T-TTTCAAGGGAAACTGTCTCAAGAGAGATAAAA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
1820514 ACGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTTGTTTCAAGGGAAATGTTTTCAATGTTTA
1820551 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1820616 ACAAAATTTGTTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTTGTTTCAAGGGAAATGTTTTCAATGTTTA
1820653 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
1820718 ACAAAATTCGTTTCAAAGGAAATGTTTTCAATGTTTA
66 ACAAAATTTGTTTCAAGGGAAATGTTTTCAATGTTTA
* *
1820755 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTTTGTTTCAAGGGAAACTATCTCAAGCGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
1820820 ATAAAAT
66 ACAAAAT
1820827 CTTCTTTTTA
Statistics
Matches: 345, Mismatches: 28, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
99 3 0.01
100 4 0.01
101 75 0.22
102 262 0.76
103 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTTGTTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:1822404 original size:69 final size:69
Alignment explanation
Indices: 1822289--1822426 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 69
1822279 TGTCTCTCTC
**
1822289 TTGATGCTCTATGATCTTCGAGTGGAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1822354 TCAT
66 TCAT
* *
1822358 TTGATGCTCTATGATCTTCGAGTAAAGTGGTTCAGTGATTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
1822423 TCAT
66 TCAT
1822427 AGTTTGAATC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (69 bp):
TTGATGCTCTATGATCTTCGAGTAAAGTGATTCAGTGATTCAGAAATGATTGTGCTTGATCAATC
TCAT
Found at i:1822521 original size:27 final size:26
Alignment explanation
Indices: 1822479--1822546 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 26
1822469 CATATGCATC
1822479 TTGTTTTCTTTT-TTTTCAGTTTTC-CT
1 TTGTTTT-TTTTCTTTTCA-TTTTCTCT
*
1822505 TTGTTTTTTTCTCTTTTTATTTTCTCT
1 TTGTTTTTTT-TCTTTTCATTTTCTCT
1822532 TTGCTTTTTTTTCTT
1 TTG-TTTTTTTTCTT
1822547 CTCTTTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
25 3 0.08
26 13 0.35
27 14 0.38
28 7 0.19
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (26 bp):
TTGTTTTTTTTCTTTTCATTTTCTCT
Found at i:1822527 original size:13 final size:14
Alignment explanation
Indices: 1822498--1822534 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1822488 TTTTTTTCAG
*
1822498 TTTTC-CTTTGTTT
1 TTTTCTCTTTGTTA
1822511 TTTTCTCTTT-TTA
1 TTTTCTCTTTGTTA
1822524 TTTTCTCTTTG
1 TTTTCTCTTTG
1822535 CTTTTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (14 bp):
TTTTCTCTTTGTTA
Found at i:1822548 original size:19 final size:18
Alignment explanation
Indices: 1822517--1822552 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1822507 GTTTTTTTCT
1822517 CTTTTTATTTTCTCTTTG
1 CTTTTTATTTTCTCTTTG
*
1822535 CTTTTTTTTCTTCTCTTT
1 CTTTTTATT-TTCTCTTT
1822553 TTGTTCTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.03, C:0.19, G:0.03, T:0.75
Consensus pattern (18 bp):
CTTTTTATTTTCTCTTTG
Found at i:1822554 original size:27 final size:26
Alignment explanation
Indices: 1822498--1822554 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
1822488 TTTTTTTCAG
*
1822498 TTTTCCTTTGTTTTTTTCTCTTTTTA
1 TTTTCCTTTGTTTTTTTCTCTTTCTA
1822524 TTTTCTCTTTGCTTTTTTT-TCTTCTCT-
1 TTTTC-CTTTG-TTTTTTTCTCTT-TCTA
1822551 TTTT
1 TTTT
1822555 GTTCTGATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.19
27 13 0.48
28 9 0.33
ACGTcount: A:0.02, C:0.18, G:0.04, T:0.77
Consensus pattern (26 bp):
TTTTCCTTTGTTTTTTTCTCTTTCTA
Found at i:1825495 original size:29 final size:28
Alignment explanation
Indices: 1825438--1825496 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
1825428 TAAAAACAAG
*
1825438 AAAAAATAGAAAATAACAAAATACGTAA
1 AAAAAATAGAAAATAACAAAATACATAA
1825466 AAAATAATA-AAAATAAACAAAATGA-ATAA
1 AAAA-AATAGAAAAT-AACAAAAT-ACATAA
1825495 AA
1 AA
1825497 TGTTAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 9 0.33
29 17 0.63
30 1 0.04
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (28 bp):
AAAAAATAGAAAATAACAAAATACATAA
Found at i:1825697 original size:10 final size:9
Alignment explanation
Indices: 1825680--1825737 Score: 53
Period size: 10 Copynumber: 5.9 Consensus size: 9
1825670 TACATGATAT
1825680 TAAAAAAAA
1 TAAAAAAAA
1825689 TAGAAAAAAA
1 TA-AAAAAAA
1825699 TAAAATAAAA
1 TAAAA-AAAA
1825709 TAAAAATATAA
1 TAAAAA-A-AA
* *
1825720 TATATATAAA
1 TA-AAAAAAA
1825730 TAAAAAAA
1 TAAAAAAA
1825738 TAGAATATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
9 10 0.25
10 23 0.57
11 5 0.12
12 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.21
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:1825745 original size:21 final size:19
Alignment explanation
Indices: 1825692--1825768 Score: 68
Period size: 21 Copynumber: 3.9 Consensus size: 19
1825682 AAAAAAATAG
1825692 AAAAAAATAAA-ATAAAAT
1 AAAAAAATAAATATAAAAT
*
1825710 AAAAATATAATATATATAAAT
1 AAAAAAATAA-ATATA-AAAT
*
1825731 AAAAAAATAGAATATTAAGA-
1 AAAAAAATA-AATA-TAAAAT
* *
1825751 AAAAATATATATATAAAA
1 AAAAAAATAAATATAAAA
1825769 ACGTATAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
18 13 0.27
19 4 0.08
20 11 0.23
21 17 0.35
22 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.25
Consensus pattern (19 bp):
AAAAAAATAAATATAAAAT
Found at i:1825753 original size:18 final size:18
Alignment explanation
Indices: 1825732--1825800 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 18
1825722 TATATAAATA
*
1825732 AAAAAATAGAATATTAAG
1 AAAAAATATAATATTAAG
*
1825750 AAAAAATATATATATAAAAACG
1 AAAAAATATA-ATAT--TAA-G
*
1825772 TATAAAATATAATATTAAG
1 -AAAAAATATAATATTAAG
1825791 AAAAAATATA
1 AAAAAATATA
1825801 TATACATAGT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
18 18 0.44
19 5 0.12
20 2 0.05
21 2 0.05
22 5 0.12
23 9 0.22
ACGTcount: A:0.67, C:0.01, G:0.06, T:0.26
Consensus pattern (18 bp):
AAAAAATATAATATTAAG
Found at i:1825755 original size:41 final size:40
Alignment explanation
Indices: 1825710--1825814 Score: 122
Period size: 41 Copynumber: 2.5 Consensus size: 40
1825700 AAAATAAAAT
1825710 AAAAATATAATATATATAAATAAAAAAATAGAATATTAAGA
1 AAAAATATAATATATATAAAT-AAAAAATAGAATATTAAGA
* * *
1825751 AAAAATAT-ATATATAAAAACGTATAAAATATAATATTAAGA
1 AAAAATATAATATATATAAA--TAAAAAATAGAATATTAAGA
*
1825792 AAAAATATATATACATAGTAAAT
1 AAAAATATA-ATATATA-TAAAT
1825815 GGAGAAAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
40 10 0.19
41 33 0.61
42 2 0.04
43 6 0.11
44 3 0.06
ACGTcount: A:0.65, C:0.02, G:0.05, T:0.29
Consensus pattern (40 bp):
AAAAATATAATATATATAAATAAAAAATAGAATATTAAGA
Found at i:1825762 original size:17 final size:18
Alignment explanation
Indices: 1825718--1825803 Score: 50
Period size: 18 Copynumber: 4.5 Consensus size: 18
1825708 ATAAAAATAT
* **
1825718 AATATATATAAATAAAAA
1 AATATATATTAACGAAAA
*
1825736 AATAGAATATTAA-GAAAA
1 AATA-TATATTAACGAAAA
*
1825754 AATATATATATAAAAACGTATAA
1 AATATATAT-T---AACG-AAAA
1825777 AATATAATATTAA-GAAAA
1 AATAT-ATATTAACGAAAA
1825795 AATATATAT
1 AATATATAT
1825804 ACATAGTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
17 8 0.15
18 21 0.39
19 7 0.13
20 2 0.04
21 2 0.04
22 1 0.02
23 9 0.17
24 4 0.07
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (18 bp):
AATATATATTAACGAAAA
Found at i:1825803 original size:43 final size:39
Alignment explanation
Indices: 1825692--1825804 Score: 117
Period size: 41 Copynumber: 2.9 Consensus size: 39
1825682 AAAAAAATAG
* * *
1825692 AAAAAAATAAAATA-AAATAAAAATATAATATATATAAAT
1 AAAAAAATAGAATATTAAGAAAAATAT-ATATATATAAAT
1825731 AAAAAAATAGAATATTAAGAAAAA-ATATATATATAAA-
1 AAAAAAATAGAATATTAAGAAAAATATATATATATAAAT
*
1825768 AACGTATAAAATATAATATTAAGAAAAA-ATATATATA
1 AA---A-AAAATAGAATATTAAGAAAAATATATATATA
1825805 CATAGTAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
37 2 0.03
38 11 0.17
39 15 0.23
40 8 0.12
41 29 0.45
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.27
Consensus pattern (39 bp):
AAAAAAATAGAATATTAAGAAAAATATATATATATAAAT
Found at i:1825886 original size:25 final size:27
Alignment explanation
Indices: 1825838--1825888 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
1825828 TACATCACAC
* *
1825838 ATATATATATATATATAATGATATAAG
1 ATATATATATATATAAAATAATATAAG
1825865 ATATATATA-ATA-AAAATAATATAA
1 ATATATATATATATAAAATAATATAA
1825889 TATCAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 3 0.14
27 9 0.41
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
ATATATATATATATAAAATAATATAAG
Found at i:1829306 original size:11 final size:11
Alignment explanation
Indices: 1829283--1829314 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1829273 TGTAATTTAT
1829283 TATTTATATATA
1 TATTTA-ATATA
1829295 TATTTAATATA
1 TATTTAATATA
1829306 TATTTAATA
1 TATTTAATA
1829315 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:1829318 original size:3 final size:3
Alignment explanation
Indices: 1829310--1829380 Score: 133
Period size: 3 Copynumber: 23.7 Consensus size: 3
1829300 AATATATATT
*
1829310 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1829358 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
1829381 TGGATAAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1829829 original size:113 final size:113
Alignment explanation
Indices: 1829691--1830363 Score: 1134
Period size: 113 Copynumber: 6.0 Consensus size: 113
1829681 TGTGATAGTA
*
1829691 TCAAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1829755 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
66 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
*
1829803 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGACGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1829868 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
66 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
1829916 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1829981 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
66 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
1830029 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * *
1830094 TCTCATTATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAAT
66 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
*** *
1830142 TCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * * *
1830207 TCTCATTATGAACTTTTTCTGGAAAAAATGATCCATCAAGTGATGAAT
66 TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
*** *
1830255 TCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * *
1830320 TCTCATTATGAACTTTCTCT-TCAAAAAATAATCCATCAATTGAT
66 TCTCATTATGAACCTTCTCTGGC-AAAAATAATCCATCAAGTGAT
1830364 AGATTTGAAT
Statistics
Matches: 543, Mismatches: 16, Indels: 3
0.97 0.03 0.01
Matches are distributed among these distances:
112 6 0.01
113 537 0.99
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (113 bp):
TCAAACAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
TCTCATTATGAACCTTCTCTGGCAAAAATAATCCATCAAGTGATGAAT
Found at i:1831089 original size:14 final size:14
Alignment explanation
Indices: 1831070--1831097 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1831060 GGTTCTGTAG
1831070 TTCCTACTAAACCA
1 TTCCTACTAAACCA
1831084 TTCCTACTAAACCA
1 TTCCTACTAAACCA
1831098 AATCAGATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (14 bp):
TTCCTACTAAACCA
Found at i:1831226 original size:52 final size:52
Alignment explanation
Indices: 1831164--1831320 Score: 305
Period size: 52 Copynumber: 3.0 Consensus size: 52
1831154 AATTCGGTGA
1831164 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
*
1831216 TTGGTTCTGTCTAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
1831268 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
1831320 T
1 T
1831321 ATTGGCAAAT
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 103 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (52 bp):
TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGC
Found at i:1831407 original size:83 final size:83
Alignment explanation
Indices: 1831268--1831603 Score: 620
Period size: 83 Copynumber: 4.0 Consensus size: 83
1831258 CAGAAGATGC
1831268 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1831333 ATCTTCTAAATTCAATGA
66 ATCTTCTAAATTCAATGA
*
1831351 TTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1831416 ATCTTCTAAATTCAATGA
66 ATCTTCTAAATTCAATGA
*
1831434 TTGGTTCTGTCTAACCAGATCTGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
1831499 ATCTTCTAAATTCAATGA
66 ATCTTCTAAATTCAATGA
* *
1831517 TTGGTTCTGTCTAACCAGATCTGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCACATT
1 TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATT
1831581 CATCTTCTAAATTCAATGA
65 CATCTTCTAAATTCAATGA
1831600 TTGG
1 TTGG
1831604 ACTAAGATAT
Statistics
Matches: 248, Mismatches: 4, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
82 2 0.01
83 246 0.99
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (83 bp):
TTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTC
ATCTTCTAAATTCAATGA
Found at i:1832757 original size:7 final size:6
Alignment explanation
Indices: 1832724--1832806 Score: 66
Period size: 6 Copynumber: 13.5 Consensus size: 6
1832714 CTTGACCCCC
*
1832724 TTTCTT TTTCTT CTCTT-TT TTTCAT TTTCTAT TTT-TT TTTC-T TTTCTTT
1 TTTCTT TTTCTT -T-TTCTT TTTCTT TTTCT-T TTTCTT TTTCTT TTTC-TT
*
1832773 TTTCTT TTCTTTCT TTTCTT TTTC-T TTTCTT TTT
1 TTTCTT TT-TCT-T TTTCTT TTTCTT TTTCTT TTT
1832807 TCTTCAAGCA
Statistics
Matches: 63, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
5 16 0.25
6 26 0.41
7 16 0.25
8 5 0.08
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:1832768 original size:5 final size:5
Alignment explanation
Indices: 1832724--1832805 Score: 62
Period size: 5 Copynumber: 15.6 Consensus size: 5
1832714 CTTGACCCCC
* *
1832724 TTTCT TTT-T CTTCT CTTT-T TTTCAT TTTCTAT TTTTT TTTCT TTTCTTT
1 TTTCT TTTCT TTTCT -TTTCT TTTC-T TTTC--T TTTCT TTTCT TTTC--T
1832773 TTTCT TTTC- TTTCT TTTCTT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTC-T TTTCT TTTCT TTT
1832806 TTCTTCAAGC
Statistics
Matches: 64, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
4 10 0.16
5 32 0.50
6 12 0.19
7 10 0.16
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:1832774 original size:16 final size:16
Alignment explanation
Indices: 1832724--1832807 Score: 98
Period size: 16 Copynumber: 4.9 Consensus size: 16
1832714 CTTGACCCCC
1832724 TTTCTTTTTCTTCTCTTTT
1 TTTC-TTTTCTT-T-TTTT
1832743 TTTCATTTTCTATTTTTT
1 TTTC-TTTTCT-TTTTTT
1832761 TTTCTTTTCTTTTTTCT
1 TTTCTTTTCTTTTTT-T
*
1832778 TTTC-TTTCTTTTCTT
1 TTTCTTTTCTTTTTTT
1832793 TTTCTTTTCTTTTTT
1 TTTCTTTTCTTTTTT
1832808 CTTCAAGCAT
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
15 5 0.08
16 23 0.39
17 11 0.19
18 8 0.14
19 11 0.19
20 1 0.02
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTCTTTTCTTTTTTT
Found at i:1832780 original size:21 final size:20
Alignment explanation
Indices: 1832724--1832805 Score: 76
Period size: 21 Copynumber: 3.9 Consensus size: 20
1832714 CTTGACCCCC
* *
1832724 TTTCTTTTTCTTCTCTTT-T
1 TTTCTTTTTCTTTTTTTTCT
*
1832743 TTTCATTTTCTATTTTTTTTTCT
1 TTTC-TTTT-T-CTTTTTTTTCT
*
1832766 TTTCTTTTTTCTTTTCTTTCT
1 TTTC-TTTTTCTTTTTTTTCT
1832787 TTTCTTTTTCTTTTCTTTT
1 TTTCTTTTTCTTTT-TTTT
1832806 TTCTTCAAGC
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
19 4 0.08
20 14 0.27
21 17 0.33
22 7 0.14
23 9 0.18
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTCTTTTTCTTTTTTTTCT
Found at i:1832795 original size:32 final size:30
Alignment explanation
Indices: 1832724--1832810 Score: 113
Period size: 32 Copynumber: 2.8 Consensus size: 30
1832714 CTTGACCCCC
*
1832724 TTTCTTTTTCTTCTCTTTTTTTCATTTTCTAT
1 TTTCTTTTTCTTTTC-TTTTTTC-TTTTCTAT
*
1832756 TTT-TTTTTCTTTTCTTTTTTCTTTTCTTTCT
1 TTTCTTTTTCTTTTCTTTTTTCTTTTC--TAT
1832787 TTTCTTTTTCTTTTCTTTTTTCTT
1 TTTCTTTTTCTTTTCTTTTTTCTT
1832811 CAAGCATAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
29 5 0.10
30 7 0.14
31 15 0.30
32 23 0.46
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (30 bp):
TTTCTTTTTCTTTTCTTTTTTCTTTTCTAT
Found at i:1845582 original size:11 final size:11
Alignment explanation
Indices: 1845559--1845590 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
1845549 TGTAATTTAT
1845559 TATTTATATATA
1 TATTTA-ATATA
1845571 TATTTAATATA
1 TATTTAATATA
1845582 TATTTAATA
1 TATTTAATA
1845591 ATAATAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:1845594 original size:3 final size:3
Alignment explanation
Indices: 1845586--1845662 Score: 145
Period size: 3 Copynumber: 25.7 Consensus size: 3
1845576 AATATATATT
*
1845586 TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1845634 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1845663 TGGATAAAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1846391 original size:15 final size:15
Alignment explanation
Indices: 1846358--1846407 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1846348 ATATATGATA
*
1846358 CGAATAACACATATC
1 CGAATAACATATATC
1846373 CGAATAACATATA-C
1 CGAATAACATATATC
*
1846387 TCGAATATCATATATC
1 -CGAATAACATATATC
*
1846403 TGAAT
1 CGAAT
1846408 TTCGATCTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (15 bp):
CGAATAACATATATC
Found at i:1849643 original size:21 final size:21
Alignment explanation
Indices: 1849619--1849666 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1849609 GTTAGGGGAG
* *
1849619 TTACGTGATGAGGTCAGTGCT
1 TTACGTGATAAGGTCAGTACT
*
1849640 TTACGTGATAAGGTCGGTACT
1 TTACGTGATAAGGTCAGTACT
1849661 TTACGT
1 TTACGT
1849667 CACAACAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (21 bp):
TTACGTGATAAGGTCAGTACT
Found at i:1849900 original size:4 final size:4
Alignment explanation
Indices: 1849891--1849932 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
1849881 TTTTTTGGTA
* * *
1849891 TTAT TTAT TTAT TTAT TTAC TGAT TTAT TTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1849933 TTAGCGGCCC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (4 bp):
TTAT
Found at i:1850104 original size:21 final size:22
Alignment explanation
Indices: 1850077--1850138 Score: 83
Period size: 21 Copynumber: 2.9 Consensus size: 22
1850067 ATTCACCTGC
1850077 CATCGTTCAAGAGGCCCCTCAT
1 CATCGTTCAAGAGGCCCCTCAT
* *
1850099 -ATCGTTCAAGATGCCCCT-GT
1 CATCGTTCAAGAGGCCCCTCAT
*
1850119 CATCGTTCAAGAGGTCCCTC
1 CATCGTTCAAGAGGCCCCTC
1850139 CCACCATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 33 0.97
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (22 bp):
CATCGTTCAAGAGGCCCCTCAT
Found at i:1851714 original size:20 final size:20
Alignment explanation
Indices: 1851689--1851736 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1851679 AATTCGTAAC
1851689 TTGACTTTTACGTTGCGAAT
1 TTGACTTTTACGTTGCGAAT
*
1851709 TTGACTTTTGCGTTGCGAAT
1 TTGACTTTTACGTTGCGAAT
1851729 TTGACTTT
1 TTGACTTT
1851737 CACAACAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.48
Consensus pattern (20 bp):
TTGACTTTTACGTTGCGAAT
Found at i:1854324 original size:24 final size:24
Alignment explanation
Indices: 1854290--1854343 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1854280 CTGAAACATC
1854290 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1854314 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1854338 ATCAAA
1 ATCAAA
1854344 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1854357 original size:24 final size:24
Alignment explanation
Indices: 1854290--1854357 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1854280 CTGAAACATC
* * *
1854290 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1854314 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1854338 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1854358 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1854939 original size:14 final size:14
Alignment explanation
Indices: 1854905--1854942 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
1854895 TTGTAAAACA
*
1854905 CCATGAACATTCTC
1 CCATGACCATTCTC
1854919 CCATGACCATTCTC
1 CCATGACCATTCTC
1854933 CCATGACCAT
1 CCATGACCAT
1854943 CCAAAACACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.26, C:0.39, G:0.08, T:0.26
Consensus pattern (14 bp):
CCATGACCATTCTC
Found at i:1855148 original size:14 final size:15
Alignment explanation
Indices: 1855112--1855151 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
1855102 GAAATCAGTG
1855112 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1855127 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1855142 AAAAATTATA
1 AAAAATTATA
1855152 GATGGGGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 8 0.36
15 4 0.18
16 10 0.45
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1855350 original size:20 final size:20
Alignment explanation
Indices: 1855325--1855437 Score: 70
Period size: 20 Copynumber: 5.6 Consensus size: 20
1855315 TTAAATTCGT
1855325 GTTGCGAATTTGAAAATTGA
1 GTTGCGAATTTGAAAATTGA
*** *
1855345 GTTGCGAA-AACAAAATTCGC
1 GTTGCGAATTTGAAAATT-GA
* *
1855365 GTTGCGAA-TTCAGAAATCGA
1 GTTGCGAATTTGA-AAATTGA
* *
1855385 GTTACGAATTTG-AAATTCAGT
1 GTTGCGAATTTGAAAATT--GA
* * *
1855406 GTTGCGAATTTGGAAATCGC
1 GTTGCGAATTTGAAAATTGA
1855426 GTTGCGAATTTG
1 GTTGCGAATTTG
1855438 GAGTTCGCGT
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
19 10 0.14
20 40 0.56
21 18 0.25
22 4 0.06
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (20 bp):
GTTGCGAATTTGAAAATTGA
Found at i:1855422 original size:41 final size:40
Alignment explanation
Indices: 1855317--1855455 Score: 134
Period size: 40 Copynumber: 3.5 Consensus size: 40
1855307 GTCAGAAATT
* * ****
1855317 AAATTCGTGTTGCGAATTTGAAAATTGAGTTGCGAAAACA
1 AAATTCGTGTTGCGAATTTGGAAATCGAGTTGCGAATTTG
* ** *
1855357 AAATTCGCGTTGCGAATTCAGAAATCGAGTTACGAATTTG
1 AAATTCGTGTTGCGAATTTGGAAATCGAGTTGCGAATTTG
*
1855397 AAATTCAGTGTTGCGAATTTGGAAATCGCGTTGCGAATTTG
1 AAATTC-GTGTTGCGAATTTGGAAATCGAGTTGCGAATTTG
* * * *
1855438 GAGTTCGCGTTACGAATT
1 AAATTCGTGTTGCGAATT
1855456 CGAGACCGCG
Statistics
Matches: 79, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 46 0.58
41 33 0.42
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (40 bp):
AAATTCGTGTTGCGAATTTGGAAATCGAGTTGCGAATTTG
Found at i:1855438 original size:20 final size:20
Alignment explanation
Indices: 1855361--1855476 Score: 101
Period size: 20 Copynumber: 5.8 Consensus size: 20
1855351 AAAACAAAAT
**
1855361 TCGCGTTGCGAATTCAGAAA
1 TCGCGTTGCGAATTTGGAAA
* *
1855381 TCGAGTTACGAATTT-GAAA
1 TCGCGTTGCGAATTTGGAAA
*
1855400 TTCAGTGTTGCGAATTTGGAAA
1 -TC-GCGTTGCGAATTTGGAAA
**
1855422 TCGCGTTGCGAATTTGGAGT
1 TCGCGTTGCGAATTTGGAAA
* * *
1855442 TCGCGTTACGAA-TTCGAGA
1 TCGCGTTGCGAATTTGGAAA
*
1855461 CCGCGTTGCGAATTTG
1 TCGCGTTGCGAATTTG
1855477 TTGGTTATTT
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
19 19 0.24
20 42 0.54
21 13 0.17
22 4 0.05
ACGTcount: A:0.25, C:0.16, G:0.28, T:0.31
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGGAAA
Found at i:1856487 original size:31 final size:31
Alignment explanation
Indices: 1856451--1856509 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1856441 AACTTAAAAG
*
1856451 AGTTTTGCAATACTAAAATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
* *
1856482 AGTTTTATAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTAAAATTTAAATAAT
1856510 CCATACAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:1856561 original size:22 final size:22
Alignment explanation
Indices: 1856533--1857073 Score: 666
Period size: 22 Copynumber: 24.6 Consensus size: 22
1856523 ATAATAATTT
1856533 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
1856555 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
1856577 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
1856599 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
1856621 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
***
1856643 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
1856665 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
* ***
1856687 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
*
1856709 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
***
1856731 TTTTAAAAT-AATTTTTTCCATA
1 TTTTAAAATAAATCAATT-CATA
*
1856753 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
1856775 TTTTAAAATAAATCAA-TCTGTA
1 TTTTAAAATAAATCAATTC-ATA
*
1856797 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
1856819 TTTTAAAATAAA--ATTTCCCATA
1 TTTTAAAATAAATCAATT--CATA
*
1856841 TTTTTAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
***
1856863 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
1856885 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
1856907 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
***
1856929 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
1856951 TTTTAAAATAAATCAA-TCAATA
1 TTTTAAAATAAATCAATTC-ATA
* ***
1856973 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATTCATA
1856995 TTTTAAAATAAATCAA-TCGATA
1 TTTTAAAATAAATCAATTC-ATA
*
1857017 TTTTAAAATAAATCAATTCGTA
1 TTTTAAAATAAATCAATTCATA
*
1857039 TTTTAAAATAAATTAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
1857061 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1857074 TTTAATAATT
Statistics
Matches: 445, Mismatches: 59, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.00
21 13 0.03
22 417 0.94
23 10 0.02
24 3 0.01
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:1860262 original size:275 final size:276
Alignment explanation
Indices: 1859770--1860320 Score: 971
Period size: 275 Copynumber: 2.0 Consensus size: 276
1859760 TATTATGAGT
1859770 AACCTCTTCATAAGCATAAGCCCTGATGTCGAAAGACAGAGTACCTTTTGCAGTGTTTCATACAG
1 AACCTCTTCATAAGCATAAGCCCTGATGTCGAAAGACAGAGTACCTTTTGCAGTGTTTCATACAG
*
1859835 CTATACTGAATTTACTTATTGTGGTCATTTCATCATTACTATTAACAAAAATGAACCATTCTGCT
66 CTATACTGAATATACTTATTGTGGTCATTTCATCATTACTATTAACAAAAATGAACCATTCTGCT
1859900 AATTTTTAGTGTTAGAGAAAATATTTATTTATACAAATGTATTGGAGAAATATGGCTGTATTTGT
131 AATTTTTAGTGTTAGAGAAAATATTTATTTATACAAATGTATTGGAGAAATATGGCTGTATTTGT
* * *
1859965 AAGAACCCATTTCCCAATAGAATTTTCTGGCTTAAGTCACACTATTTACACCTGTTGTTATGTTA
196 AAGAACCCATTTCCCAATAGAATTTTCTGGCTTAAGTCACACCATTTACACCTGTTCTCATGTTA
1860030 ACTCTATAGCCTACTA
261 ACTCTATAGCCTACTA
*
1860046 AACCTCTTCATAAGCATAAGCCCTGATGTCGAAAGACAGAGTACCTTTTGCAAG-GTTTCATTCA
1 AACCTCTTCATAAGCATAAGCCCTGATGTCGAAAGACAGAGTACCTTTTGC-AGTGTTTCATACA
* * *
1860110 GCTCTACTGAATATACTTATTGTGGT-ATTTCATCATTACTATTGACAAAAATGAACTATTCTGC
65 GCTATACTGAATATACTTATTGTGGTCATTTCATCATTACTATTAACAAAAATGAACCATTCTGC
* * *
1860174 TAATTTTTAGTGTTAGAGAAAATATTTATTTGTGCAAATGTGTTGGAGAAATATGGCTGTATTTG
130 TAATTTTTAGTGTTAGAGAAAATATTTATTTATACAAATGTATTGGAGAAATATGGCTGTATTTG
*
1860239 TAAGAACCCATTTCCTAATAGAATTTTCTGGCTTAAGTCACACCATTTACACCTGTTCTCATGTT
195 TAAGAACCCATTTCCCAATAGAATTTTCTGGCTTAAGTCACACCATTTACACCTGTTCTCATGTT
1860304 AACTCTATAGCCTACTA
260 AACTCTATAGCCTACTA
1860321 TGTTACCATG
Statistics
Matches: 262, Mismatches: 12, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
275 176 0.67
276 84 0.32
277 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (276 bp):
AACCTCTTCATAAGCATAAGCCCTGATGTCGAAAGACAGAGTACCTTTTGCAGTGTTTCATACAG
CTATACTGAATATACTTATTGTGGTCATTTCATCATTACTATTAACAAAAATGAACCATTCTGCT
AATTTTTAGTGTTAGAGAAAATATTTATTTATACAAATGTATTGGAGAAATATGGCTGTATTTGT
AAGAACCCATTTCCCAATAGAATTTTCTGGCTTAAGTCACACCATTTACACCTGTTCTCATGTTA
ACTCTATAGCCTACTA
Done.